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Fix unhandled exceptions in MSA parsing and PDB serialization #1124

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Fix unhandled exceptions in MSA parsing and PDB serialization #1124

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3 changes: 2 additions & 1 deletion alphafold/common/protein.py
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Original file line number Diff line number Diff line change
Expand Up @@ -297,7 +297,8 @@ def to_pdb(prot: Protein) -> str:
charge = ''
# PDB is a columnar format, every space matters here!
atom_line = (
f'{record_type:<6}{atom_index:>5} {name:<4}{alt_loc:>1}'
display_index = atom_index % 100000
f'{record_type:<6}{display_index:>5} {name:<4}{alt_loc:>1}'
f'{res_name_3:>3} {chain_ids[chain_index[i]]:>1}'
f'{residue_index[i]:>4}{insertion_code:>1} '
f'{pos[0]:>8.3f}{pos[1]:>8.3f}{pos[2]:>8.3f}'
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5 changes: 5 additions & 0 deletions alphafold/data/parsers.py
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Expand Up @@ -140,6 +140,11 @@ def parse_stockholm(stockholm_string: str) -> Msa:
keep_columns = [i for i, res in enumerate(query) if res != '-']

# Remove the columns with gaps in the query from all sequences.
if keep_columns and len(sequence) <= max(keep_columns):
raise ValueError(
f'Malformed MSA: Hit sequence length ({len(sequence)}) is strictly '
f'shorter than required columns ({max(keep_columns)}).'
)
aligned_sequence = ''.join([sequence[c] for c in keep_columns])

msa.append(aligned_sequence)
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